Welcome to Tractor!
For a comprehensive understanding of Tractor's methodology and application, we invite you to read our following 2021 Nature Genetics publication here.
Atkinson, E.G., Maihofer, A.X., Kanai, M. et al. Tractor uses local ancestry to enable the inclusion of admixed individuals in GWAS and to boost power. Nat Genet 53, 195–204 (2021).
We also recently developed Tractor-Mix, which enables modeling admixture with relatedness. Please refer to our preprint here.
Tan T, Vergara-Lope A, Martínez-Magaña JJ, Shah NN, Yuan K, Berumen J, Alegre-Díaz J, Kuri-Morales P, Tapia-Conyer R, Gelenter J, Montalvo-Ortiz JL, Zhou W, Torres JM, Atkinson EG. Extending Genome-Wide Association Studies to admixed cohorts with high degrees of relatedness. medRxiv [Preprint]. 2025 Jun 9:2025.05.27.25328444. doi: 10.1101/2025.05.27.25328444. PMID: 40585113; PMCID: PMC12204420.
To facilitate users in implementing the method, we've curated a series of tutorials available here. These tutorials cover each step of the Tractor pipeline using a toy dataset. Please download and unzip the provided file with the toy data to follow along.
Please note that while this tutorial offers a high-level guide to running Tractor/Tractor-Mix, users are advised to ensure the reliability and accuracy of phasing and local ancestry inference, as these factors influence the Tractor GWAS results.
- Step 0: Phasing and Local Ancestry Inference
- Step 1: Recovering Tracts
- Step 2: Extracting tracts and ancestry dosages
- Step 3a: Tractor GWAS with local implementation (suitable for smaller dataset)
- Step 3b: Tractor GWAS with Hail (suitable for large scale analysis)
- Step 4: Visualization of Tractor summary statistics
- Step 0: Phasing and Local Ancestry Inference
- Step 1: Recovering Tracts (often skipped)
- Step 2: Extracting tracts and ancestry dosages
- Step 3: Estimate PC/GRM
- Step 4: Mixed effect model with Tractor-Mix